Police conducted early morning operations at the homes of some of the academics, according to local Turkish media. The number who will be detained is expected to rise.
The government accuses them of a range of charges, from "making propaganda on behalf of a terrorist organization" to "denigrating" the Turkish people and authorities, according to state news agency Anadolu.
The petition, released on Monday, called for "the state to abandon its deliberate massacre and deportation of Kurdish and other peoples in the region. We also demand the state to lift the curfew, punish those who are responsible for human rights violations, and compensate those citizens who have experienced material and psychological damage."
A ceasefire broke down between the Kurdistan Workers' Party (PKK) and government last June, reigniting the 30-year-old conflict when an ISIS suicide bomber killed more than 30 people. The PKK blamed the government for colluding with ISIS in the attack and assassinated two police officers in their homes. The government hit back by bombing PKK strongholds in northern Iraq. Since then the fight has moved into the cities in the predominantly Kurdish southeast.
Turkey has imposed curfews, some lasting for days, while conducting operations in predominately Kurdish neighborhoods and towns in the southeast. The government says it is to clear those areas of militants and dismantle barricades set up by a youth wing of the PKK.
Scores have been killed in the fighting, including civilians who've been caught in the crossfire.
Critics of the government argue that the operations have amounted to collective punishment for residents living in areas where the operations are being conducted.
"It has attacked these settlements with heavy weapons and equipment that would only be mobilized in wartime," the petition stated. "As a result, the right to life, liberty, and security, and in particular the prohibition of torture and ill-treatment protected by the constitution and international conventions have been violated."
Some universities have begun their own internal investigations of academics who have signed the declaration, according to Turkish media.
Ceren Uysal, a lawyer with the Progressive Lawyers Association who is looking into the detentions, called the allegations against the academics "completely lawless."
"There is nothing to constitute a crime in this declaration. Our constitution, and international agreements that Turkey is a part of, protect the freedom of speech and expression. This petition does not call for violence. It is just a criticism.
"Nothing in it consitutues a crime within the law."
The government views the petition as an effort to legitimize the actions of the PKK, which they say takes the declaration from being a freedom expression issue to supporting the group, which is designated as a terrorist organization by Turkey, the United States and the European Union.
A Turkish official, speaking on condition of anonymity, said the declaration contains "no single sentence referring to the actions of the PKK, no single sentence referring to the killing of civilians by the PKK, no sentence condemning such actions."
"The problem is that when you do not refer to one single act of the PKK, when you do not take a position against their activities which are universally defined as terrorist activities, there is no meaning for a position to claim that it is part of free speech," the official said.
Turkish President Recep Tayyip Erdogan lashed out at the signatories, calling on all government branches to punish those "who benefit from the state but act as enemies of the state."
Referring to the allegations in the petition, Erdogan said, "Because of the actions of the terrorist organization the rights and freedoms of millions of our citizens are being violated. But the ones doing these violations are not the state, it is the terrorist organization itself."
In the past, intellectuals have become targets for ultranationalists after public hearings on "anti-Turkishness" or "insulting the Turkish Republic." That the president openly called for punishment of the signatories has had a chilling effect.
Sedat Peker, an ultranationalist leader and former crime boss, has threatened the signatories of the declaration.
"We will drain your blood in streams, and we will shower in your gushing blood," Peker wrote on his personal website.
The names and photographs of the academics have been circulated on pro-government social media accounts. While many of the academics fear for their safety, the government insists that they'll take every necessary step to protect them.
"Launching an investigation process is one thing, and putting them in a fragile position is another," said a Turkish official.